Giulio Poli and Tiziano Tuccinardi * Pages 182 - 190 ( 9 )
Background: Molecular docking is probably the most popular and profitable approach in computer-aided drug design, being the staple technique for predicting the binding mode of bioactive compounds and for performing receptor-based virtual screening studies. The growing attention received by docking, as well as the need for improving its reliability in pose prediction and virtual screening performance, has led to the development of a wide plethora of new docking algorithms and scoring functions. Nevertheless, it is unlikely to identify a single procedure outperforming the other ones in terms of reliability and accuracy or demonstrating to be generally suitable for all kinds of protein targets.
Methods: In this context, consensus docking approaches are taking hold in computer-aided drug design. These computational protocols consist in docking ligands using multiple docking methods and then comparing the binding poses predicted for the same ligand by the different methods. This analysis is usually carried out calculating the root-mean-square deviation among the different docking results obtained for each ligand, in order to identify the number of docking methods producing the same binding pose.
Results: The consensus docking approaches demonstrated to improve the quality of docking and virtual screening results compared to the single docking methods. From a qualitative point of view, the improvement in pose prediction accuracy was obtained by prioritizing ligand binding poses produced by a high number of docking methods, whereas with regards to virtual screening studies, high hit rates were obtained by prioritizing the compounds showing a high level of pose consensus.
Conclusion: In this review, we provide an overview of the results obtained from the performance assessment of various consensus docking protocols and we illustrate successful case studies where consensus docking has been applied in virtual screening studies.
Consensus docking, molecular modeling, virtual screening, docking reliability, computer-aided drug design, scoring functions.
Department of Pharmacy, University of Pisa, Pisa, Department of Pharmacy, University of Pisa, Pisa